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. 2020 Mar 12;7(1):90.
doi: 10.1038/s41597-020-0426-6.

Draft genomes of female and male turbot Scophthalmus maximus

Xi-Wen Xu #  1   2 , Chang-Wei Shao #  1   2 , Hao Xu #  1   3 , Qian Zhou  1   2 , Feng You  4 , Na Wang  1   2 , Wen-Long Li  1 , Ming Li  1   3 , Song-Lin Chen  5   6
Affiliations

Draft genomes of female and male turbot Scophthalmus maximus

Xi-Wen Xu et al. Sci Data. .

Abstract

Turbot (Scophthalmus maximus) is a commercially important flatfish species in aquaculture. It has a drastic sexual dimorphism, with females growing faster than males. In the present study, we sequenced and de novo assembled female and male turbot genomes. The assembled female genome was 568 Mb (scaffold N50, 6.2 Mb, BUSCO 97.4%), and the male genome was 584 Mb (scaffold N50, 5.9 Mb, BUSCO 96.6%). Using two genetic maps, we anchored female scaffolds representing 535 Mb onto 22 chromosomes. Annotation of the female anchored genome identified 87.8 Mb transposon elements and 20,134 genes. We identified 17,936 gene families, of which 369 gene families were flatfish specific. Phylogenetic analysis showed that the turbot, Japanese flounder and Chinese tongue sole form a clade that diverged from other teleosts approximately 78 Mya. This report of female and male turbot draft genomes and annotated genes provides a new resource for identifying sex determination genes, elucidating the evolution of adaptive traits in flatfish and developing genetic techniques to increase the sustainability of turbot aquaculture.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Paraffin sectioning and HE staining of gonadal tissues of the female and male turbot. (a) Section of the ovary. (b) Section of the testis.
Fig. 2
Fig. 2
Comparisons of gene parameters among Scophthalmus maximus, Danio rerio, Paralichthys olivaceus, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes, Tetraodon nigroviridis and Homo sapiens genomes. (a) Gene length distributions of the species. (b) CDS length distributions of the species. (c) Exon number distributions of the species. (d) Exon length distributions of the species. (e) Intron length distributions of the species. Y-axis of (a,b,d,e) stand for density, while Y-axis of (c) stands for ratio of genes.
Fig. 3
Fig. 3
Venn diagram of the numbers of unique and shared gene families among nine sequenced teleost species.
Fig. 4
Fig. 4
Evolution of orthologous gene families and their estimated divergence times in nine teleost species. The blue numbers on the nodes are the divergence times in million years ago (Mya). The red circles indicated the calibration time.
Fig. 5
Fig. 5
Circos graph of whole-genome synteny analysis for female genome and the reference genome of turbot.
See this image and copyright information in PMC

References

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